8SCB: Terminating ribosome with SRI-41315
Terminating ribosome with SRI-41315. Determined by electron microscopy at 2.5 Å resolution. Released 27 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 2.5 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens
- Chains
- 87
- Atoms
- 222,478
- Mol. weight
- 3615.29 kDa
- Ligands
- SF4, ZVM, ZN, MG
- Released
- 27 Dec 2023
Explore 8SCB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8SCB contains 618 α-helices and 604 β-strands across 79 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain a: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 7-10 | 4 | |
| α-helix | 42-48 | 7 | |
| α-helix | 65-68 | 4 | |
| β-strand | 72-74 | 3 | 188 |
| α-helix | 75-77 | 3 | |
| α-helix | 79-81 | 3 | |
| α-helix | 84-90 | 7 | |
| β-strand | 98 | 1 | 116 |
| β-strand | 100-102 | 3 | 189 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 188 |
| β-strand | 123-126 | 4 | 189 |
| β-strand | 128-129 | 2 | 188 |
| α-helix | 131-139 | 9 | |
| β-strand | 143-146 | 4 | 189 |
Chain A: 13 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-5 | 2 | |
| α-helix | 8-11 | 4 | |
| α-helix | 14-16 | 3 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-49 | 9 | 1 |
| β-strand | 58-64 | 7 | 1 |
| β-strand | 71-77 | 7 | 1 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 2 |
| β-strand | 83 | 1 | 3 |
| β-strand | 87-90 | 4 | 1 |
| β-strand | 101-103 | 3 | 1 |
| α-helix | 104-106 | 3 | |
| α-helix | 108 | 1 | |
| β-strand | 112-114 | 3 | 1 |
| β-strand | 116 | 1 | 4 |
| β-strand | 126 | 1 | 4 |
| β-strand | 134-140 | 7 | 1 |
| β-strand | 145-149 | 5 | 1 |
| β-strand | 155-159 | 5 | 1 |
| β-strand | 163-166 | 4 | 1 |
| β-strand | 169 | 1 | 2 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| α-helix | 201-203 | 3 | |
| α-helix | 206-208 | 3 | |
| β-strand | 224-225 | 2 | 5 |
| α-helix | 229-230 | 2 | |
| β-strand | 237-238 | 2 | 5 |
Chain aa: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 192 |
| β-strand | 29-31 | 3 | 192 |
| β-strand | 36-43 | 8 | 193 |
| α-helix | 47-49 | 3 | |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 131 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 193 |
| α-helix | 75-81 | 7 | |
| α-helix | 89-92 | 4 | |
Chain AA: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 190 |
| α-helix | 34-37 | 4 | |
| β-strand | 38-41 | 4 | 190 |
| β-strand | 47-49 | 3 | 190 |
| α-helix | 51-67 | 17 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 191 |
| α-helix | 81-94 | 14 | |
| α-helix | 96 | 1 | |
| β-strand | 97-100 | 4 | 191 |
| α-helix | 103-104 | 2 | |
| β-strand | 121-124 | 4 | 191 |
| α-helix | 131-137 | 7 | |
| β-strand | 144-148 | 5 | 191 |
| β-strand | 159-162 | 4 | 191 |
| α-helix | 168-186 | 19 | |
| α-helix | 199-202 | 4 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 22-24 | 3 | |
| α-helix | 37-48 | 12 | |
| α-helix | 54-75 | 22 | |
Chain B: 23 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 14-16 | 3 | |
| α-helix | 20-22 | 3 | |
| α-helix | 27-28 | 2 | |
| α-helix | 32-34 | 3 | |
| α-helix | 40-41 | 2 | |
| β-strand | 42-43 | 2 | 11 |
| β-strand | 45-59 | 15 | 12 |
| β-strand | 71-80 | 10 | 12 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 13 |
| β-strand | 98-106 | 9 | 13 |
| α-helix | 112-117 | 6 | |
| α-helix | 122-124 | 3 | |
| α-helix | 131-134 | 4 | |
| α-helix | 135-137 | 3 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 13 |
| α-helix | 168-170 | 3 | |
| β-strand | 180-184 | 5 | 13 |
| β-strand | 185-186 | 2 | 11 |
| α-helix | 190-200 | 11 | |
| β-strand | 204-205 | 2 | 13 |
| α-helix | 207-210 | 4 | |
| β-strand | 216-222 | 7 | 12 |
| α-helix | 223-224 | 2 | |
| β-strand | 225-229 | 5 | 14 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-273 | 4 | 14 |
| β-strand | 276-288 | 13 | 12 |
| α-helix | 289-291 | 3 | |
| β-strand | 292-293 | 2 | 15 |
| β-strand | 297-298 | 2 | 15 |
| α-helix | 316 | 1 | |
| β-strand | 320 | 1 | 16 |
| β-strand | 324 | 1 | 16 |
| β-strand | 330-334 | 5 | 12 |
| β-strand | 344-349 | 6 | 12 |
| α-helix | 357-360 | 4 | |
| α-helix | 361-363 | 3 | |
| β-strand | 365-368 | 4 | 12 |
| α-helix | 382-389 | 8 | |
Chain bb: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| β-strand | 32-36 | 5 | 8 |
| β-strand | 43-47 | 5 | 8 |
| β-strand | 55 | 1 | 9 |
| β-strand | 62 | 1 | 9 |
| β-strand | 65 | 1 | 10 |
| β-strand | 72 | 1 | 10 |
| α-helix | 73-74 | 2 | |
| β-strand | 78-81 | 4 | 8 |
Chain BB: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-34 | 7 | 6 |
| β-strand | 45-50 | 6 | 6 |
| α-helix | 51-52 | 2 | |
| β-strand | 53 | 1 | 7 |
| β-strand | 56 | 1 | 7 |
| α-helix | 58-62 | 5 | |
| β-strand | 66-70 | 5 | 6 |
| α-helix | 71-74 | 4 | |
| β-strand | 82-91 | 10 | 6 |
| β-strand | 95-105 | 11 | 6 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 6 |
| β-strand | 134-143 | 10 | 6 |
| α-helix | 155-157 | 3 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 207-219 | 13 | 6 |
| α-helix | 225-232 | 8 | |
71 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ribosomal protein L8 | A | protein | 257 | Oryctolagus cuniculus | G1TT27 (AlphaFold model) |
| Ribosomal protein L3 | B | protein | 403 | Oryctolagus cuniculus | G1TL06 (AlphaFold model) |
| 60S ribosomal protein L4 | C | protein | 413 | Oryctolagus cuniculus | G1SVW5 (AlphaFold model) |
| Ribosomal_L18_c domain-containing protein | D | protein | 297 | Oryctolagus cuniculus | P19949 (AlphaFold model) |
| 60S ribosomal protein L6 | E | protein | 291 | Oryctolagus cuniculus | G1SKF7 |
| 60S ribosomal protein L7 | F | protein | 247 | Oryctolagus cuniculus | G1TUB1 |
| 60S ribosomal protein L7a | G | protein | 319 | Oryctolagus cuniculus | G1STW0 |
| 60S ribosomal protein L9 | H | protein | 192 | Oryctolagus cuniculus | G1SWI6 |
| 60S ribosomal protein L10 | I | protein | 214 | Oryctolagus cuniculus | B7NZQ2 |
| 60S ribosomal protein L11 | J | protein | 178 | Oryctolagus cuniculus | G1TUB8 |
| eL13 | L | protein | 211 | Oryctolagus cuniculus | |
| 60S ribosomal protein L14 | M | protein | 218 | Oryctolagus cuniculus | G1SZ12 |
75 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8SCB_1 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>8SCB_2 Ribosomal protein L3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 3 (C), FASTA
>8SCB_3 60S ribosomal protein L4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA
Sequence of entity 4 (D), FASTA
>8SCB_4 Ribosomal_L18_c domain-containing protein (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>8SCB_5 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 6 (F), FASTA
>8SCB_6 60S ribosomal protein L7 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN
Sequence of entity 7 (G), FASTA
>8SCB_7 60S ribosomal protein L7a (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG
Sequence of entity 8 (H), FASTA
>8SCB_8 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 9 (I), FASTA
>8SCB_9 60S ribosomal protein L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>8SCB_10 60S ribosomal protein L11 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 11 (L), FASTA
>8SCB_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (M), FASTA
>8SCB_12 60S ribosomal protein L14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| ZVM | (2S,4aS)-2-cyclobutyl-10-methyl-3-phenyl-2,10-dihydropyrimido[4,5-b]quinoline-4… | C22 H21 N3 O2 | 1 |
| ZN | Zinc ion | Zn | 8 |
| MG | Magnesium ion | Mg | 312 |
Primary citation
The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. Coelho, J.P.L., Yip, M.C.J., Oltion, K. et al. Nat Chem Biol (2024) 20:877-884. DOI 10.1038/s41589-023-01521-0 · PubMed
Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
- 9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
- 9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
- 8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
- 6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
- 7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
- 9BDL 2.8 Å, 80S ribosome with angiogenin
- 9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
- 9NDP 2.82 Å, Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC
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